Driving east on 101 as you approach the town of Exeter, you’ll see three huge man-made lagoons filled with dirty looking water.

Sitting on top of the water are strange looking metal machines.

If you’ve ever wondered what all that is, Jennifer Perry says you wouldn’t be alone.

“People are saying, what is that? (laughs) Well, it’s the wastewater treatment plant. (laughs) It’s been here quite a few years, since the 60’s.”

Perry is Exeter’s Public Works Director.

“Originally they were smaller lagoons and they were built up, we expanded them after a few years to just increase our capacity.”

Each of these lagoons covers nine acres, is ten feet deep, and holds up to 28 million gallons of treated wastewater.

Scott Miller, the Chief Operator for the plant, says those those metal things floating on the water are aerators and circulators.

“It circulates the water and disperses the sediments, the sludge, so it’s not just in a certain area, and it breaks down a lot easier if it’s all dispersed.”

Miller says on an average day, the plant treats about two million gallons of wastewater.

“Our permits are based off of three million gallons a day, but peak seven and a half, but we’ve put out closer to nine million in one day when we’ve had back to back 100 year floods, storms and stuff."

Reporter: " So where does this discharge?"

" Right over there in the Squamscott River, where that blue sign is.”

The blue sign warns boaters of where the sewage discharges.

The Squamscott River, Perry says, eventually flows into the Great Bay.

“At low tide, it’s a lot of mudflats, even at the lowest tide you can’t see the outfall, it’s submerged, even at the lowest tides.”

But Exeter’s aerated lagoons provide only what’s called primary treatment.

And under primary treatment, the plant is not required to remove nitrogen.

Both the EPA and the New Hampshire Department of Environmental Services say excess nitrogen is what’s polluting the Great Bay.

And that pollution, say researchers, is killing the bay’s eelgrass, a vital habitat and food source for wildlife.

Perry expects the EPA to issue a new permit for the plant, and it will include new limits on total nitrogen, which are often called nutrients.

“The new nutrient standard is going to mean the town is going to have to step up to the plate and design and construct a new facility or significant facility to be able to meet those new standards.”

The new tougher federal standards won’t affect just Exeter, but all 14 New Hampshire wastewater treatment plants in the Great Bay watershed, and several in Maine.

In total, 20 million gallons of wastewater is dumped into the Great Bay every day.

For most of the treatment plants, the more the EPA limits nitrogen, the more it costs.

Perry says Exeter’s lagoons can discharge as much as 30 milligrams per liter of nitrogen.

“Say if we had to meet 10 milligrams per liter total nitrogen, we could probably do that with some fairly straightforward modifications to our existing aerated lagoons, but if we had to get down to five, that’s a whole nother animal, we’d probably have to have multiple processes that would have to be added.”

But Paul Currier says the EPA could ask Exeter to remove even more nitrogen.

Currier is Watershed Administrator for the state Department of Environmental Services.

“The safest thing for a permit writer to do is to put permit limits in permits that are the limit of technology which is three milligrams per liter, the most nitrogen that can be removed with a process that you can design and build today.”

But Jennifer Perry says paying for those upgrades would likely double the sewer rates.

The City of Portsmouth is facing a similar but more urgent problem.

For several years, their old treatment plant on Peirce Island, which was built in 1964, has violated the Clean Water Act.

The city is under a legal agreement with the EPA to upgrade, which will likely mean relocating all of their wastewater treatment to Pease International Tradeport.

At a public meeting to explain the plan to residents, Peter Goodwin, an engineering consultant for Portsmouth, says it won’t be cheap.

“When you’re making decisions of this magnitude you really need to be looking at life cycle costs… if you put 122.9 million dollars in the bank today, you would have the dollar value you need to construct and operate these facilities for 20 years.”

But the new nitrogen limits could add even more cost, tripling sewer fees to two thousand dollars a year for the average residential user.

And under the Clean Water Act, federal officials do not have to consider costs when setting permit limits for wastewater treatment plants.

But Carl DeLoi, EPA’s New Hampshire Director, says they recognize that affordability is an issue.

He says the EPA could phase in limits, so the cost is spread over time.

“So if somebody said you had to reach three milligrams per liter and you had to do it in two years, the impact to the community would be much different than if you said ten years.”

But sewer treatment officials feel they’re being unfairly targeted, considering nitrogen from treatment plants accounts for only a third of the problem in the Great Bay.

Peter Rice is Portsmouth’s city engineer.

“Obviously the development, land use, and surface runoff issues, the non point sources are really what’s driving this problem, and our resources and our efforts really should be driven in that direction.”

He says it’s easier for the EPA to go after treatment plants because they’re already regulated.

Rice says Portsmouth has also hired a Washington, DC-based consultant who questions whether nitrogen is the cause of the Great Bay’s problems. J

ohn Hall, with Hall and Associates, presented those findings to residents in Portsmouth.

He called the research the state used overly simplified.

“If you use these simplified approaches, you can misdirect scarce resources, I tell you for Great Bay, the worst of the situation could be you could spend a lot of the money over a ten to 15 year period and then you could turn around and look at the Bay and see that it’s not improved.”

Hall says a host of other problems could be impacting eelgrass loss, not just excess nutrients.

New Hampshire DES and the Piscataqua Regions Estuary Partnership, or PREP, agree nitrogen isn’t the only factor effecting eelgrass loss.

But PREP Coastal Scientist Phil Trowbridge says it’s enough of a problem that it shouldn’t be ignored.

“PREP is very supportive of the idea of continuing to study the issues and use good and objective science and to reach consensus among all parties, however we should not delay implementing common sense solutions right away, the longer we wait, the worst the problem will be, the more expensive it will be to fix, and our chances of success will be lower.”

Trowbridge says it’s just as important to target other sources of nitrogen pollution in the Great Bay- the non point sources like stormwater runoff which account for two-thirds of the problem.

But he says that’s a more difficult task, and one that could take decades.